@sjcrh/proteinpaint-server 2.127.0 → 2.128.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.127.0",
+  "version": "2.128.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -65,7 +65,7 @@
     "@sjcrh/proteinpaint-r": "2.126.2",
     "@sjcrh/proteinpaint-rust": "2.126.2",
     "@sjcrh/proteinpaint-shared": "2.126.0",
-    "@sjcrh/proteinpaint-types": "2.126.1",
+    "@sjcrh/proteinpaint-types": "2.128.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdcGRIN2list.js

@@ -1,19 +1,20 @@
-import { gdcMafPayload } from "#types/checkers";
+import { gdcGRIN2listPayload } from "#types/checkers";
 import ky from "ky";
 import { joinUrl } from "#shared/joinUrl.js";
 import serverconfig from "#src/serverconfig.js";
 const maxFileNumber = 1e3;
 const allowedWorkflowType = "Aliquot Ensemble Somatic Variant Merging and Masking";
+const maxFileSizeAllowed = 1e6;
 const maxTotalSizeCompressed = serverconfig.features.gdcMafMaxFileSize || 4e8;
 const api = {
   endpoint: "gdc/GRIN2list",
   methods: {
     get: {
-      ...gdcMafPayload,
+      ...gdcGRIN2listPayload,
       init
     },
     post: {
-      ...gdcMafPayload,
+      ...gdcGRIN2listPayload,
       init
     }
   }
@@ -84,6 +85,8 @@ async function listMafFiles(q, ds) {
     const c = h.cases?.[0];
     if (!c)
       throw "h.cases[0] missing";
+    if (h.file_size >= maxFileSizeAllowed)
+      continue;
     const file = {
       id: h.id,
       project_id: c.project.project_id,

package/routes/gdcGRIN2run.js

@@ -31,53 +31,43 @@ function init({ genomes }) {
       if (!caseFiles) {
         throw "Missing or invalid cases data";
       }
+      console.log("[GRIN2] Calling Rust for file processing...");
+      const rustInput = JSON.stringify(caseFiles);
+      console.log("[GRIN2] Executing Rust function...");
+      const rustResult = await run_rust("gdcGRIN2", rustInput);
+      console.log("[GRIN2] Rust execution completed");
+      if (!rustResult) {
+        throw new Error("Failed to process MAF files: No result from Rust");
+      }
+      let parsedRustResult;
+      try {
+        parsedRustResult = typeof rustResult === "string" ? JSON.parse(rustResult) : rustResult;
+        console.log(`[GRIN2] Parsed Rust result: ${JSON.stringify(parsedRustResult).substring(0, 200)}...`);
+      } catch (parseError) {
+        console.error("[GRIN2] Error parsing Rust result:", parseError);
+      }
+      const genedbfile = path.join(serverconfig.tpmasterdir, g.genedb.dbfile);
+      const imagefile = path.join(serverconfig.cachedir, `grin2_${Date.now()}_${Math.floor(Math.random() * 1e9)}.png`);
+      const rInput = JSON.stringify({
+        genedb: genedbfile,
+        chromosomelist: g.majorchr,
+        imagefile,
+        lesion: rustResult
+        // The mutation string from Rust
+      });
+      console.log(`R input: ${rInput}`);
+      console.log("[GRIN2] Executing R script...");
+      const rResult = await run_R("gdcGRIN2.R", rInput, []);
+      console.log(`[GRIN2] R execution completed, result: ${rResult}`);
+      let resultData;
       try {
-        console.log("[GRIN2] Calling Rust for file processing...");
-        const rustInput = JSON.stringify(caseFiles);
-        console.log("[GRIN2] Executing Rust function...");
-        const rustResult = await run_rust("gdcGRIN2", rustInput);
-        console.log("[GRIN2] Rust execution completed");
-        console.log(`[GRIN2] Rust result type: ${typeof rustResult}`);
-        if (!rustResult) {
-          throw new Error("Failed to process MAF files: No result from Rust");
-        }
-        let parsedRustResult;
-        try {
-          parsedRustResult = typeof rustResult === "string" ? JSON.parse(rustResult) : rustResult;
-          console.log(`[GRIN2] Parsed Rust result: ${JSON.stringify(parsedRustResult).substring(0, 200)}...`);
-        } catch (parseError) {
-          console.error("[GRIN2] Error parsing Rust result:", parseError);
-        }
-        const genedbfile = path.join(serverconfig.tpmasterdir, g.genedb.dbfile);
-        const imagefile = path.join(serverconfig.cachedir, `grin2_${Date.now()}_${Math.floor(Math.random() * 1e9)}.png`);
-        const rInput = JSON.stringify({
-          genedb: genedbfile,
-          chromosomelist: g.majorchr,
-          imagefile,
-          lesion: rustResult
-          // The mutation string from Rust
-        });
-        console.log(`R input: ${rInput}`);
-        const parsedInput = JSON.parse(rInput);
-        console.log("Parsed lesion data type:", typeof parsedInput.lesion);
-        console.log(
-          "Parsed lesion data length:",
-          typeof parsedInput.lesion === "string" ? parsedInput.lesion.length : "not a string"
-        );
-        console.log("[GRIN2] Executing R script...");
-        const rResult = await run_R("gdcGRIN2.R", rInput, []);
-        console.log(`[GRIN2] R execution completed, result: ${rResult}`);
-        let resultData;
-        try {
-          resultData = JSON.parse(rResult);
-          console.log("[GRIN2] Finished R analysis");
-          const pngImg = resultData.png[0];
-          return res.json({ pngImg });
-        } catch (parseError) {
-          console.error("[GRIN2] Error parsing R result:", parseError);
-          console.log("[GRIN2] Raw R result:", rResult);
-        }
-      } finally {
+        resultData = JSON.parse(rResult);
+        console.log("[GRIN2] Finished R analysis");
+        const pngImg = resultData.png[0];
+        return res.json({ pngImg });
+      } catch (parseError) {
+        console.error("[GRIN2] Error parsing R result:", parseError);
+        console.log("[GRIN2] Raw R result:", rResult);
       }
     } catch (e) {
       console.error("[GRIN2] Error running analysis:", e);